Our initial plan was to base NEM on the NXT code, which is why there are two versions of the NXT code in the repository. However, this project garnered a really large amount of interest and we have more dev resources than I expected. At this time, it is the consensus of the dev team to base NEM on some of the NXT ideas but write the code from scratch. While this will take a little more time and effort now, I think it will set up NEM much better in the long run.
The goal is not for NEM to be a NXT copy and paste coin. IMO, there's no value in that. With NEM, we want to take some of the best ideas of NXT and Bitcoin and create something new and, hopefully, better.
My only criticisms of writing the code from scratch are:
(a) Won't be as well tested and stable as a NXT clone.
(b) May cause people to lose interest and NEM to lose momentum if it takes too long to complete.
But other than that, it's a great idea!